Using protein-protein interaction network information to predict the subcellular locations of proteins in budding yeast

Protein Pept Lett. 2012 Jun 1;19(6):644-51. doi: 10.2174/092986612800494066.

Abstract

The information of protein subcellular localization is vitally important for in-depth understanding the intricate pathways that regulate biological processes at the cellular level. With the rapidly increasing number of newly found protein sequence in the Post-Genomic Age, many automated methods have been developed attempting to help annotate their subcellular locations in a timely manner. However, very few of them were developed using the protein-protein interaction (PPI) network information. In this paper, we have introduced a new concept called "tethering potential" by which the PPI information can be effectively fused into the formulation for protein samples. Based on such a network frame, a new predictor called Yeast-PLoc has been developed for identifying budding yeast proteins among their 19 subcellular location sites. Meanwhile, a purely sequence-based approach, called the "hybrid-property" method, is integrated into Yeast-PLoc as a fall-back to deal with those proteins without sufficient PPI information. The overall success rate by the jackknife test on the 4,683 yeast proteins in the training dataset was 70.25%. Furthermore, it was shown that the success rate by Yeast- PLoc on an independent dataset was remarkably higher than those by some other existing predictors, indicating that the current approach by incorporating the PPI information is quite promising. As a user-friendly web-server, Yeast-PLoc is freely accessible at http://yeastloc.biosino.org/.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Databases, Protein
  • Intracellular Space / metabolism
  • Models, Statistical
  • Protein Interaction Maps
  • Proteome / metabolism
  • Proteomics / methods*
  • Saccharomyces cerevisiae / cytology
  • Saccharomyces cerevisiae / metabolism*
  • Saccharomyces cerevisiae Proteins / chemistry
  • Saccharomyces cerevisiae Proteins / metabolism*
  • Software
  • Subcellular Fractions / chemistry
  • Subcellular Fractions / metabolism

Substances

  • Proteome
  • Saccharomyces cerevisiae Proteins